One of the most widely used techniques to study gene expression exploits first-strand cDNA of mRNA sequence(s) as a template for PCR amplification. The ability to measure the kinetics of a PCR reaction in combination with reverse transcriptase-PCR techniques promises to facilitate the accurate and precise measurement of target RNA sequences with the requisite level of sensitivity. In particular, fluorescent dual-labeled hybridization probe technologies, such as the “CATACLEAVE™ endonuclease assay (described in detail in U.S. Pat. No. 5,763,181; see FIG. 1), permit the detection of reverse transcriptase-PCR amplification in real-time. Detection of target sequences is achieved by including a CATACLEAVE™ probe in the amplification reaction together with RNAse H. The CATACLEAVE™ probe, which is complementary to a target sequence within the reverse transcriptase-PCR amplification product, has a chimeric structure comprising an RNA sequence and a DNA sequence, and is flanked at its 5′ and 3′ ends by a detectable marker, for example FRET pair labeled DNA sequences. The proximity of the FRET pair's fluorescent label to the quencher precludes fluorescence of the intact probe. Upon annealing of the probe to the reverse transcriptase-PCR product a RNA: DNA duplex is generated that can be cleaved by RNAse H present in the reaction mixture. Cleavage within the RNA portion of the annealed probe results in the separation of the fluorescent label from the quencher and a subsequent emission of fluorescence.